Benthos LPI Surveys

Overview

The Line Point Intercept (LPI) protocol is used to quantify benthic community composition at Pristine Seas UVS sites. Divers swim along a fixed transect line and record the benthic taxon or category directly beneath a series of regularly spaced sampling points.

Points are recorded every 20 cm along a 50-meter transect, yielding 250 point intercepts per station, typically divided into five 10-meter sections (50 points each). In some cases, shorter transects (e.g., 30 m) are used, resulting in fewer total points.

This method yields high-resolution estimates of percent cover for key benthic groups—such as hard coral, macroalgae, crustose coralline algae (CCA), and cyanobacteria—and supports assessments of reef condition and spatial variability.

LPI data are organized across three interlinked tables:

• uvs.lpi_stations - Metadata and summary metrics for each LPI transect station
• uvs.lpi_counts - Point intercept counts per morphotaxon, station, and section
• uvs.lpi_cover_by_taxa - Percent cover summaries by taxon or functional group, per station

All records are linked via ps_station_id. Taxa are harmonized using accepted_name and accepted_aphia_id, which represent the minimum resolved taxonomic level per morphotaxon.

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Tables

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Stations (uvs.lpi_stations)

Each row in this table represents a single depth-stratified LPI survey at a UVS site. Fields include spatial and habitat metadata, survey effort (e.g., transect length, number of sections, total points), and benthic summary metrics such as percent cover of hard coral, CCA, and cyanobacteria.

Table 1: Schema for uvs.lpi_stations: metadata and summary metrics for each LPI transect station

Field	Type	Required	Description
ps_station_id	STRING	true	Unique station ID (ps_site_id_depth).
ps_site_id	STRING	true	Foreign key to uvs.sites.
exp_id	STRING	true	Expedition ID (ISO3_YEAR).
method	STRING	true	Survey method (uvs).
protocol	STRING	true	Survey protocol (benthic_lpi).
divers	STRING	true	Divers who conducted the LPI transects.
region	STRING	true	Region name.
subregion	STRING	true	Subregion name.
locality	STRING	false	Optional local feature (e.g., reef, bay).
latitude	FLOAT	true	Latitude of station (decimal degrees, WGS84).
longitude	FLOAT	true	Longitude of station (decimal degrees, WGS84).
date	DATE	true	Date of LPI survey.
time	TIME	true	Start time of the LPI transects (24-hour format).
depth_m	FLOAT	true	Average station depth (m).
depth_strata	STRING	true	Depth bin: supershallow, shallow, or deep.
habitat	STRING	true	Habitat type (e.g., fore reef, patch reef).
exposure	STRING	true	Exposure type (e.g., windward, leeward, lagoon).
transect_distance	INTEGER	true	Total length of transect surveyed (m).
n_sections	INTEGER	true	Number of 10m sections surveyed (typically 5).
n_points	INTEGER	true	Total number of points sampled across all transects.
pct_coral	FLOAT	false	Percent of points classified as hard coral (Scleractinia).
pct_cca	FLOAT	false	Percent of points classified as crustose coralline algae (CCA).
pct_cyano	FLOAT	false	Percent of points classified as cyanobacteria.
notes	STRING	false	Optional QA or field notes.

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Counts (uvs.lpi_counts)

This table stores summarized point intercept data from LPI transects. Each row represents the number of points at which a given morphotaxon was recorded within a specific station and transect section.

Each record includes:

• A diver-entered morphotaxon label (e.g., “Porites sp.”, “CCA”, “Turf”)
• A standardized accepted_name and accepted_aphia_id (minimum taxonomic resolution)
• A functional group classification (e.g., coral, CCA, macroalgae)

The n_points field indicates how many times the morphotaxon was recorded in the section. This format supports fine-scale spatial summaries while preserving compatibility with aggregate-level analyses.

Table 2: Schema for uvs.lpi_counts: point intercept counts by morphotaxon and transect section

Field	Type	Required	Description
ps_station_id	STRING	true	Foreign key linking to uvs.lpi_stations.
diver	STRING	true	Name of the diver who recorded the data.
station_label	STRING	true	Field-assigned stratum label (e.g., shallow, deep).
depth_m	FLOAT	true	Recorded depth (m) at which the LPI transect was conducted.
section	INTEGER	true	Transect section number (typically 1–5 for 10 m intervals).
morphotaxon	STRING	true	Field-entered morphotaxon label (e.g., ‘Porites sp.’, ‘CCA’, ‘Turf’).
accepted_name	STRING	true	Standardized scientific name representing the minimum identifiable taxon.
accepted_aphia_id	INTEGER	true	WoRMS AphiaID — foreign key to taxonomy.benthic.
functional_group	STRING	true	Functional group classification (e.g., coral, CCA, turf, macroalgae).
n_points	INTEGER	true	Number of point intercepts assigned to the morphotaxon in the given section.
notes	STRING	false	Optional comments or QA annotations.

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Cover by Taxa (uvs.lpi_cover_by_taxa)

This table contains station-level summaries of benthic percent cover by taxon or group. Each row represents a unique combination of ps_station_id and benthic taxon, with cover calculated as the proportion of total points assigned to that taxon.

Taxonomic identity is standardized via accepted_name and accepted_aphia_id. Functional group assignments support grouped summaries such as total coral, algae, or CCA cover, and are consistent with those used across reef condition assessments and visualizations.

Table 3: Schema for uvs.lpi_cover_by_taxa: percent cover by taxon at each LPI station

Field	Type	Required	Description
ps_station_id	STRING	true	Unique station ID (ps_site_id_depth), e.g., CHL_2024_uvs_001_20m.
accepted_name	STRING	true	Scientific name of the benthic taxon (Genus species) or category.
accepted_aphia_id	INTEGER	true	Unique AphiaID from WoRMS; foreign key to taxonomy.benthic.
functional_group	STRING	true	Functional group classification (e.g., coral, CCA, turf, macroalgae).
depth_m	FLOAT	true	Mean depth (m) of the station.
depth_strata	STRING	true	Depth bin label: supershallow, shallow, or deep.
region	STRING	true	Region name.
subregion	STRING	true	Subregion (e.g., island, gulf, reef complex).
locality	STRING	false	Optional local feature (e.g., reef, bay, cove).
habitat	STRING	true	Dominant habitat type at the station.
exposure	STRING	true	Wave/wind exposure at the station (windward, leeward, lagoon).
n_points	INTEGER	true	Total number of point intercepts assigned to the taxon.
pct_cover	FLOAT	true	Percent cover calculated as n_points divided by total points at the station * 100.